Linting and Style Checks
========================

This repo includes ``.clang-tidy`` and ``.clang-format`` at the root, plus
MRtrix-inspired helper scripts for formatting and style checks.

Prerequisites
-------------

- ``clang-format`` available on ``PATH``
  - macOS (Homebrew): ``brew install llvm`` (or ``llvm@17``) and ensure
    ``clang-format`` is on ``PATH``
  - Ubuntu: ``sudo apt-get install clang-format``
- For ``check_syntax`` on macOS, GNU grep is required (``brew install grep``,
  then it will use ``ggrep``).

clang-format (bulk formatting)
------------------------------

.. code-block:: bash

   ./clang-format-all

You can target a specific clang-format binary:

.. code-block:: bash

   ./clang-format-all --executable /path/to/clang-format

check_syntax (style rules)
--------------------------

Run the MRtrix-style checks against the C++ sources:

.. code-block:: bash

   ./check_syntax

Results are written to ``syntax.log`` when issues are found.

clang-tidy
----------

Generate a build with compile commands, then run clang-tidy (matches CI):

.. code-block:: bash

   cmake -S . -B build \
     -DTRX_USE_CONAN=OFF \
     -DTRX_BUILD_EXAMPLES=ON \
     -DCMAKE_EXPORT_COMPILE_COMMANDS=ON
   run-clang-tidy -p build $(git ls-files '*.cpp' '*.h' '*.hpp' '*.tpp' ':!third_party/**')

To run clang-tidy automatically during builds:

.. code-block:: bash

   cmake -S . -B build -DTRX_ENABLE_CLANG_TIDY=ON
   cmake --build build

If you have ``run-clang-tidy`` installed (LLVM extras), you can lint everything
tracked by the repo (excluding ``third_party``), which matches CI.